SNAKE Eyes
by Reveries In Red
Summary: Ever since the Ayano, the Founder of the Mekakushi Organization faked her death, her spy organization has had to lie low to survive. Now that Shintaro, their sleeper agent has finally recovered his memories, the time to take down SNAKE once and for all has finally arrived. Based on NinthFeather's Spy AU
1. Chapter 1

A/N: This fanfiction is based on NinthFeather's Spy AU in _Reset the World_. Ayano is the founder of a spy organization, and the original Mekakushi Dan are her top agents.

* * *

Visions of better days danced in her head.

Ayano remembered when she met Tsubomi, Kousuke and Shuuya for the first time – how terrified they had been and how cheerful her attitude used to be. Life had been so simple before she found out her father had joined SNAKE, a top secret terrorist organization and scientific facility that performed gruesome and unethical experiments on human subjects. She remembered having a small laugh over how "SNAKE" seemed like an awfully similar name to "Hydra" and briefly wondered if she was a S.H.I.E.L.D agent living in the Marvel Universe. Of course, that joy died once Ayano realized the full extent of her father's experimentation.

The brunette shook her head out of her thoughts before focusing her dull brown gaze on the multitude of monitors before her, her eyes darting between the different camera angles as she soaked in the information displayed before her. This had been her daily life since she faked her death two years ago. Once again, Ayano shook herself out of her thoughts and forced herself to pay attention to her computer screens. Her "suicide" wasn't exactly pleasant to think about. Of course, Ayano's motivations as founder of the Mekakushi Organization were nothing but altruistic, but watching as everyone who knew her suffered and tortured themselves over her loss had been a horrible experience. Shintaro, her currently amnesiac sleeper agent who had walked into her cameras' line of vision, still hadn't seemed to have recovered. Her gaze followed him as he wandered into Marry's room, walking past the former SNAKE agent's sleeping form and moving to inspect a photograph sitting on her dresser.

"Ayano...?"

Ayano cringed as Shintaro collapsed onto the ground with a crash. Upon zooming in, she noticed that his eyes were brimming with tears, but this was far from the first time she had watched him cry over her. At first, she was tempted to contact him and let him know that she wasn't dead, but after two years of almost zero human interaction, acts like these didn't seem to faze her anymore.

The noise startled Marry out of her sleep, and she seemed equally surprised to find that Shintaro had _already_ made it in her room. After all, according to the plan Ayano made before she fled off to her bunker, Shintaro's being in Marry's room – the heart of the organization's headquarters – meant that he had gained the trust of the Mekakushi Organization's members and that he was worthy of having his original memories restored to him. This meant that the recovery mission was now moving in full motion after two years of preparations. _No pressure..._

"Shintaro?" The former SNAKE agent called, trying to hide her nervousness.

The sleeper agent immediately sat up from his position on the floor, momentarily forgetting about his dead friend. "M-Marry? I, um, I wasn't being creepy, I was just..." He trailed off, refusing to look at anything but the floor. Shintaro swore he could feel eyes burning holes into his back.

Marry plopped down in front of Shintaro, watching him carefully and half noticing how pathetic he looked. She supposed she couldn't exactly blame him though, since she was the only one that knew that Ayano's death had been faked, but even Marry had no idea of Ayano's whereabouts. She was barely aware of the cameras Ayano had installed in every corner of the headquarters. "Shintaro, look at me."

The new recruit – or so he thought –, slowly turned his bloodshot gaze towards the seemingly younger girl.

"I want you to hold still. I'm going to give you your memories back," Marry produced two round electronic devices from her apron's pocket and stuck one on each side of Shintaro's head.

"Huh? Wait, whoa!" After staring at her with confused eyes, Shintaro finally processed that he did not want this machine to touch him and attempted to pull them off, but to no avail. "I haven't lost any memories – and what did you just stick on me?!" In fact, he remembered them more vividly than ever, much to his chagrin. Amazing how all it took was a photograph to trigger bright red memories of a warm smile...

"Oh, you designed these!" Marry grinned. It was weird to finally know more than the boy genius; she'd have to cherish this moment while it lasted. "You called it Invention 0707. I never really understood your explanation of how it worked, but you mentioned something about sending certain stimuli to the hippocampus in order to manipulate the creation of new memories. You used it because you said you'd be better at strategizing if you could remember every detail about everything," she paused, mentally verifying her explanation. "Oh, and you don't think you're amnesiac because we've replaced your missing memories. If I remember correctly, you think you went to school with Director Ayano, right? You think you met her when she changed desks in order to sit next to you. And, because she had bad grades, she made you tutor her. Right?"

"Yeah…?" Shintaro stared at Marry, almost frozen in shock. He _invented_ that? Well, it was a genius idea he supposed, so it wasn't all that surprising. But, what happened to the adorable little fluff girl side of Marry? He knew they were secret agents and all, but now that seemed like a guise to hide her enormous depths of knowledge. "If that's not what happened, then what's _your_ version of events?"

"I suppose you're about to find out," Marry flicked a switch on one of the devices stuck to his temple and turned some dials on the other. "Alright. I want you to close your eyes and think about everything you know about Director Ayano. You have to be able to visualize her for this to work properly."

"No problem..." Shintaro grumbled. As much as he hated it, he could picture his first friend in an instant; he had almost every single detail memorized, from the exact shade of her irises to the way her teeth would show through her goofy grins. Ugh. Why was he agreeing to this again?

"3... 2... 1..."

Shintaro stiffened, feeling the electricity buzzing through his head – okay, what _was_ this, a Sci-Fi movie?! – and suddenly, he could picture her again, but in a completely different set of circumstances. Marry was right. That whole school scenario seemed way too romantic to be true, which likely stemmed from his closet adoration of shoujo manga. Oh no, exactly how much did Marry know about him...? She didn't know about his secret folders, did she? A sudden feeling of dread washed over him.

"Well?" Marry smiled, but it only unnerved him even more. "How did you _really_ meet her?"

"I... She was in need of a strategist for her 'Mekakushi Organization'. I think she called me a _Tactician_ or something. I never really understood the name, but she said it was a video game reference," Shintaro paused, remembering the gleeful look on her face. What was the game called? Emblem of Flames? The point was, this girl certainly didn't seem like a mob boss, or whatever her official title was. "We met through Kido, since she was a mutual contact between my sister and Ayano. I was in need of a job, and Ayano provided me with one." Their relationship was supposed to be strictly professional, but his boss treated all her employees like personal friends. It always bothered him, but he remembered warming up to her a little before she...

Marry removed the circular devices from his head with a pop and stored them back in her pocket. "So, now you should remember agreeing to be our sleeper agent in case anything happened to Director Ayano or the Mekakushi Organization, right?"

"Yeah, but why now? That _something_ happened to Ayano two years ago."

Marry opened her mouth, unsure of how to phrase their mission without giving away Ayano's status, but in a stroke of pure luck, someone burst into the room, swiftly interrupting her.

"Where's Kido?!" A girl with her cerulean hair tied into asymmetrical pigtails peered around Marry's room, shooting her fellow agents a weird look upon discovering them sitting together on the ground. "Um..."

"I think Director Kido is debriefing Seto about a new weapon proposal. What's the matter, Ene?" Marry responded, standing up and dusting off her dress.

"I just found the coordinates of a secret SNAKE bunker!" Ene exclaimed, looking both excited and distressed. "It's almost scary how close it is to our headquarters, actually."

Marry's eyes widened, her mass of white hair seeming to twitch with anxiety. "Oh... Director Kido will want to know about this immediately. I think she's in the common room."

"Thanks!" Ene turned to leave but stopped and shot Shintaro a glare. "Don't try anything weird, you pervert."

"I wasn't–" Before he could finish though, Ene had vanished from sight. "I'm going to follow her. Kido will want to strategize with me," the black-haired boy announced, eager to get out of the hellhole that was Marry's room. What _exactly_ was her relationship with Ayano?

He supposed it didn't matter, though. Ayano was dead.


	2. Chapter 2

Upon reaching the common room, Shintaro found that Kido and Ene already seemed to be discussing Ene's new discovery.

"An attack is too risky," Kido's stern voice echoed slightly in the giant room. "The signal you found could easily be some sort of trap – it just seems too obvious."

Ene's eyes seemed to widen in a desperate attempt to convince her boss. "But what if it isn't? This could be our one chance to gain an upper hand on SNAKE! They'd never see it coming!"

The green-haired director pursed her lips together. It had been two years and Shintaro _still_ hadn't gotten his memories back, not to mention that Ene usually had good instincts. She knew that this plan was the last project Ayano had worked on before she died, but Kido felt like a sitting duck from all this waiting. "Alright, but let's make it a small scale attack. We can't afford to keep waiting for Marry to give Shintaro his memories back anymore."

Shintaro coughed awkwardly into his sleeve, figuring now was as good a time as ever to interrupt their conversation. "Marry gave me my memories back," The strategist announced, crossing his arms as he walked into the common room. "But anyway, we would definitely have the element of surprise on our hands if we attacked, not to mention that you guys have two years' worth of unused supplies and weapons. We could take over this base and use it to intercept other SNAKE messages. We'd probably have a couple days to stay there and gather materials until they realized that one of their communication hubs has been hijacked. We're going to want to relocate to a temporary base on the opposite side of our original headquarters, though. This place isn't exactly subtle."

"So, you're saying that we should relocate everyone to a different base?" Kido leaned forward a little, adjusting her sitting position to accommodate. After seeing Shintaro be completely clueless since they "recruited" him a couple weeks ago, him seeming to know what he was talking about was completely bizarre.

"Yes. We've been here too long. The odds of this base being compromised are only going to increase with every day that we stay here."

Ene stared at him, looking mildly offended. "Are you calling me incompetent, Kisaragi?!" She was great at completely erasing their presence, in her opinion. Their force fields were better than they had ever been, so even if by some off chance they _were_ discovered, SNAKE would never be able to penetrate their base on her watch.

"Shush, you two," Kido knew she had to stop this argument before it spiraled out of hand like it always did. "I'll compromise with you two. I will allow you two to coordinate an attack on this base, but you must take Konoha with you two. Get in there, scope out what you can, and get back here. We're going to be vulnerable during the relocation process, so we need to be certain that we won't be attacked."

"Wait, who said _I_ was going? And Konoha is just a prototype! He doesn't even work correctly!" Shintaro complained, earning him death glares from both women at once. Two birds, one stone.

"You need to go because you need to practice field missions. You've been off the hook for two years, and–"

"–Konoha works just fine, asshole!" Ene interrupted, her fury evident through her floating pigtails. Just because the android she built had a shoddy memory system didn't mean he was incapable of kicking a certain someone's rear end. "Besides, it's not like you're one to talk! You didn't even get _your_ memories back until two minutes ago!"

"Okay, but I'm not a sh–"

Kido slammed her foot onto the ground. "–Enough! Both of you! You are to be back here in three hours, and I expect you both to be fully prepared for this mission. Understood?"

"Understood," Shintaro and Ene grumbled in unison, refusing to look at each other.

* * *

Ene stomped back to her lab, grumbling insults about how Shintaro didn't know anything and that he had no right to judge Konoha. Her coding was perfect, so why didn't it work? Ugh, programming. She would fix one bug and fifteen more would replace it. The blue haired technology expert sat down in front of her fancy computer and began typing away before she rolled her chair over to boot up Konoha.

"Eneeee~!" An annoying voice called into her room, causing the said agent to tense up in frustration at being interrupted.

"What do you want, Kano?"

Kano wandered over to her desk, making an obviously fake pouty face. "Aww, that's not a very nice way to greet someone who has valuable information!"

"What kind of valuable information?" Ene gazed at him with her peripheral vision, her glare still apparent through her scrunched up facial features.

"It's about SNAKE's new android designs. They have officially surpassed the uncanny valley," Kano reported gravely. "They can basically act as high functioning humans – their five senses have been hypersensitized and completely enhanced, not to mention that there's no way these androids could be told apart from humans except by looking into their pupils. One thing that the SNAKE engineering team couldn't fix was the command system. They send orders to the android via displaying messages in front of their pupils, so when they're receiving commands, it will look like there are thin, white lines streaking across the android's eyes. Other than that, these robots have passed the Turing test with flying colors. They can supposedly experience a wide range of complex emotions the way a human does and are able to spot said emotions in others."

What little color Ene had drained from her face. "How have they _already_ figured that out?" Whatever semblance of a good mood that she might have had was officially gone for the day. "You know what – screw them. Konoha is going to be better than their stupid androids by far!" She bragged despite knowing that achieving that would be near impossible, turning a few dials and knobs on his headphones and watching as he blinked to life, his pink eyes glowing slightly.

"Who are you...?" The soft voice seemed to reach out for Ene. Luckily, she had been through this so many times that she could recite this conversation backwards and forwards.

"I'm Ene, your creator. That kid over there is Kano – he's a nuisance," She jerked her thumb in the blond's general direction.

"Hey!" Kano protested, though it was obvious that he wasn't offended.

Ene smirked before continuing. "You work for the Mekakushi Organization, and our rivals are SNAKE agents. Whenever you see one in battle, you are to end them unless your orders state otherwise. Understand?"

Konoha nodded, staring blankly at her. "... Orders?"

"Yes, that's when I or Director Kido tell you what to do. You will _not_ listen to anyone else. You will be able to hear your orders through your headphones," Ene tapped them with her index finger, causing the android to flinch, "–so make sure to memorize my voice and Director Kido's voice."

"Who's Director Kido?" Konoha mumbled, his eyes widening in curiosity.

"She's tall, green hair, has a death stare that could kill thousands. But anyway, your first mission will be in a couple of hours. This will likely be the one time that I ever accompany you in person, so don't get used to the special treatment."

"Ooh, a mission?" Kano stuffed his hands in his pockets and leaned over, giving Ene what could have been interpreted as a flirty look but wasn't – this was Kano, after all. He flirted with anything that breathed. "Can I come?"

"No. Unfortunately, it's just going to be me, Shintaro, and this hunk of junk," Ene patted Konoha's shoulder. Konoha assumed it was a friendly human gesture and patted Ene's shoulder in return, knocking her to the ground with his strength.

"Konoha…" The first time he had done that, Ene had been livid, but after a few hundred more times of being bruised beyond relief, she was honestly more surprised that she had forgotten about his habit of imitating her this time around. Not to mention, she was getting ready to beat some sense into the stupid cat-eyed kid that had the gall to _laugh_.

"S-Sorry!" The albino android stuttered, looking at his hands in surprise. "I didn't know…"

"Nah, you're good. Kano, on the other hand… not so much," Ene glared daggers in his direction, which Konoha seemed to understand as a nonverbal message and began to chase Kano out of the room, mumbling things like 'Bad kitty!' and 'Be nice to Ene!'.

Ene rested her head on the floor with an exasperated sigh. Would Konoha ever end up the way she wanted him to?

" _Haruka…_ "


	3. Chapter 3

After yet another debriefing from Kido, Shintaro found himself stuck in one of the Mekakushi Organization's spy vehicles as he awaited their arrival at this supposed SNAKE base. He stared out the window, wishing he could just go home and sleep. He did _not_ sign up for this. The vehicle would have been comfortable enough he supposed, if Ene hadn't called shotgun and left him stuck in the backseat with Konoha, whose head mashed into the roof whenever they hit a bump. Shintaro wasn't exactly comfortable with the driver though; he looked like he was about twelve years old!

"He'd better hope Kido's invisi-tech actually works, or we're getting pulled over for sure," Shintaro grumbled, unaware of the fact that he had given voice to his thoughts.

"Hey, shut up back there," The driver glared at his rear-view mirror. "I was hand-selected by Director Kido to be in charge of building these vehicles, integrating her invisi-tech, and transporting you field agents–"

"–I'm not a field agent. I am a tactician. I'm only here because–"

"–Can you two _shut up?!_ " Ene whipped around, glaring daggers at Shintaro. "Hibiya, just focus on the damn road before you get us into a wreck. I would appreciate not getting hit by a truck today, thanks."

Hibiya opened his mouth to argue but closed it upon realizing that Ene was technically his senior agent and that she had a point.

Shintaro groaned and went back to staring out the window, trying not to cry out in pain when the confused Konoha reached over to 'pat' his shoulder.

* * *

Once they had finally arrived at a reasonable distance away from the base, Shintaro practically jumped out of the car, eager to get his throbbing shoulder away from the belligerent android. He didn't care what Ene said – that machine was out to lop his arm off. Upon being dropped off in the forest, Shintaro and Ene promptly equipped their red eyepieces, thus activating Kido's so-called invisi-tech. According to her, it worked by bending light around the individual wearing the eyepiece or the vehicle with its integration and thus created a sort of mirror. By bending light molecules from the surrounding area around them, they thus reflected the background image, which made them "invisible". Director Kido was always sure to remind them that they weren't untouchable, so if they bumped into anyone, they were sure to be caught. With that in mind, Shintaro trudged ahead, grumbling to himself instead of waiting for Ene to finish activating Konoha's invisibility.

"Hey, wait up! What do you think you're doing?" Ene hissed, dragging Konoha forward.

"Not wasting our time. The sooner we get there, the sooner we can take out whoever's in charge and get this over with!"

"Hmph," Ene looked away, not wanting to admit that she agreed. Despite it being her idea, something about this mission seemed sort of off to her. Why hadn't they run into any scouters yet? Where were all the traps? Even the base itself looked abandoned once she and Shintaro had finally arrived. Vegetation had sprung all over the cracked walls and the doors and windows seemed rusted shut. Maybe she had been wrong...? Ene looked up at Konoha, who was busy fiddling with a leaf that had fallen into his white hair.

"Konoha," she commanded, "Check the building for any signs of life or other androids. If there's nothing within range, open the door."

Her android nodded, tucking the leave into his sleeve and approaching the door, his eyes glowing red as he did a heat-scan through the walls, creating a mental map of the place. "There is something on the top floor. It is probably a large animal."

Something was terribly suspicious about this. "Alright. Open the door."

Konoha obeyed, jerking the knob. He hadn't expected it to open so easily and ended up slamming it against the wall.

" _Konoha_! Be quiet!" Shintaro scolded, looking like a deer in headlights. "What if that person wakes up?!"

"Shintaro, shut up! That wasn't his fault!" It was all Ene could do to not beat him up. "Just get in there! You scout the top floor and I'll do everything else."

"Why do _I_ have to do the top floor! I'm _not_ going up and facing whatever animal is up there!"

"It's sleeping!" Konoha chimed in, looking proud of himself.

"You heard him! Just go up there and taser it or something!" Takane crossed her arms.

"Fine! But I'm getting the credit for this mission!"

"Whatever! Do it – just do it!"

Shintaro and Ene shot each other one last glare before he marched up the stairs as quietly as possible. He hated his life. This mission was stupid, and he had no reason to be here. The idiots were the ones that they sent on field missions because they were expendable! There was a reason that he wasn't a field agent. He actually had knowledge that was useful, but nooo, Director Kido _had_ to make him go. Besides, this whole ordeal was fishy as crap. It just had to be some sort of a trap. Why was he even here? After checking through a few rooms and finding nothing in particular, Shintaro approached the last room in the hallway, preparing his taser gun for the animal that would inevitably be in this final room. He took a huge breath and opened the door. The noise seemed to awake the illuminated shape sitting in front of the biggest set of monitors Shintaro had ever seen. Upon remembering that the animal couldn't see him, he took a few steps forward. The closer he got, the more this "animal" seemed to look more like a human. The person turned toward Shintaro, her cold gaze piercing right through him. "Hello."

Even her voice was familiar. Once he noticed her grayed brown hair, sunken eyes, and dull scarf, Shintaro yelped and instinctively pulled the trigger. He leaned forward to inspect the girl's limp body with wide eyes. Did he just taser a ghost? Why the _hell_ did this girl look just like Ayano Tateyama?


End file.
